ArticleNature microbiology2025
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.
Article in Nature microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed.
- Why probiotics fail: gut niche tension as the missing variable?Gut microbes · 2026Review
- Animal gut microbes and microbiomes in the 21st century and beyond.Science China. Life sciences · 2026Review
- An engineered bacterial symbiont maps micron-scale sugar gradients in the honeybee gut.PLoS biology · 2026Article
- The Escherichia coli uhp two-component system functions as a sensory channel for hexose phosphates secreted by Bifidobacterium.Scientific reports · 2026Article
- Micro-scale spatial metagenomics opens a new era in microbiome ecology.Trends in microbiology · 2026Review
- Profiling the gut resistome to unlock antimicrobial resistance biology and inform clinical risk.Nature communications · 2026Review
- Droplet microfluidics strategies for overcoming bottlenecks in antibiotics discovery.iScience · 2026Review
- Architectural intelligence: toward a spatial framework for interpreting microbiome-associated human disease.The ISME journal · 2026Article
- Small-scale biogeography of biofilms and its implications for sequencing-based studies.ISME communications · 2026Article
- Microbiogeographic insights as keys to understanding personalized gut microbiota responses: the role ofBioscience of microbiota, food and health · 2026Review
- MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data.Microbiome · 2025Article
- Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.Science (New York, N.Y.) · 2025Article
- Macroecological Laws Can Naturally Arise from Chaotic Internal Species Dynamics.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
- Erratum issued
- Update of
Authors and funding
12 authors.
Funding
Abstract
The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.